Swords and secrets
by Elli452
Summary: When everything has changed, how does John cope with a world without Elizabeth? And who is trapped in a world of the past? Implied character death. No spoilers. AU. Set approximately season 2. Rated T for possible bad language and mild violence later on
1. Chapter 1

Disclaimer: I don't own Atlantis, wish I did, I need the money

A/N: This is my first fanfic, more chapters to follow, be gentle…..

Thanks go out to Djara, my beta, can't write without you

Chapter 1

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The darkness was fading into a pale grey mist, and feeling was coming back. The slow, dull throb became an ache, and finally a sharp slicing pain that made her wish the darkness would come back again. A small whimper was all it took for them to realise she was conscious, the pain intensified, and the darkness came again.

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John paced Elizabeth's office, swearing under his breath. He still called it Elizabeth's office, he was the only one that did. It was his way of feeling less alone, even though she'd been gone for over six months now.

He was muttering about the uselessness of scientists when Dr. Laura Mayer, the new civilian leader appeared.

"You'll wear a hole in my floor Colonel." She admonished.

"Any news?"

"Not as yet, she's still missing; they're doing their best Colonel."

'Their best isn't good enough' John thought mutinously, whilst replying with "Fine!" And marching stiffly out of the office, no longer feeling comfortable in it.

He couldn't stand to be near Dr. Mayer any longer than was absolutely necessary, at a little over five feet, blonde and severe; she was everything Elizabeth wasn't, including a leader. The military had been consigned to the bottom ranks, dogsbodies, there to fetch and carry for the civilian and scientific personnel. He hated her.

The original team had been split up, McKay now resided with the research team, the greatest mind on Atlantis was being wasted looking at rock samples and mouldy plants. Teyla returned to the Athosians on the mainland, couldn't cope with the loss of Elizabeth enough to stay. Ronan was employed in training everyone for hand-to-hand combat; Dr. Mayer didn't consider him 'trustworthy' enough to have on a military team.

Whilst that alone would have been bad enough, She had to bring others of her type back with her. Kavanaugh was the new lead scientist in Rodney's stead, and a handful of her own 'special people' were now occupying all the top spots in the city.

One of these people was Dr. Emily Turner, who at 23 was the youngest scientist John had ever met. She didn't act like the rest of them, she was normal, no airs and graces, or supercilious attitudes, she didn't put letters after her name, or pretend she knew everything, she even asked for help every now and again. In a way, she was like Elizabeth, and that hurt like hell.

Elizabeth. He'd seen her die, he saw the bullet hit her in the chest, saw her fall into the water. Forced through the gate, he couldn't get to her, there was no way. That moment, the moment she died played over in his head from the second he shut his eyes at night, in a way he welcomed seeing it, at least he got to see her everyday still, even if it was only in his nightmares.

Sheppard was striding with such purpose that he walked straight into Col. Caldwell, who had just arrived with the Dedalus, "They've not found her then." Caldwell stated, not bothering that Sheppard had just trod on his foot.

"No, she's still 'missing'" John responded, tugging a hand through his hair, a mixture of sarcasm and resignation tinged his words.

Caldwell sighed, feeling sorry for the younger man, "They'll find her Colonel, they want to. Besides," he said jerking his head towards the office, "She wants her back, and what she wants…well you know the rest."

"Too well, only too well." John gave a brief smile, and a nod of thanks before going in search of Dr. Beckett, Carson wanted to see if he was sleeping any better, and John wasn't looking forward to telling him it had actually gotten worse.

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She was awake again, but lay still on her side so they wouldn't know, the coppery tang of blood welled in her mouth and she wanted to gag. Slowly she opened her mouth and the blood dribbled out, to join the sticky pool already surrounding her. She didn't know how long she'd been there, or even her own name, all she knew was that she wanted so desperately to go home.

Suddenly a boot connected with her spine, her head swam, and darkness fell once more.

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Carson Beckett looked up as the shadow like figure of John Sheppard walked into the infirmary. 'No good news then' he thought, shaking his head slightly, before going to greet the colonel.

"Colonel Sheppard, you look like hell." Was the Scot's opening comment, as he led him to the nearest cubicle, "If you try to tell me you've been sleeping properly, I'll sedate you right here."

"Nice to see you too doc," Sheppard said sarcastically, but without his trademark grin, "but you're right, I've not slept."

"You can't help her like this John, I've told you, your body needs rest."

"She's lost Carson, she needs to come home, any way she can." Sheppard hung his head; no words could explain how he was feeling and why he couldn't sleep. He slumped back against the bed, "It shouldn't have happened Carson; she should still be here."

Judging by the defeat and sheer exhaustion in his voice, Carson could tell this was going beyond the current situation; he was punishing himself for more than he would admit to.

"I'm going to give you a sedative now, just a light one to help you drift off, if you won't sleep in your own time, you will on mine." Said the doctor, loading a syringe and injecting him, "Just relax."

Sheppard felt the drugs taking effect, but he didn't fight them, he waited to see Elizabeth but she never came, he saw something else. A girl with short dark hair laughing, dancing over an alien landscape, so happy to be free of the confines of the lab, then the sound of hooves, horses, men with swords, darkness, pain, screaming, heat, blood, pain, screaming, heat, blood, pain, screaming, heat, bloo…"EMILY!"

He leapt from the bed as though it were aflame, his heart was pounding so fast and the adrenaline rushing at such a speed, he didn't hear Carson shout his name. Then it was all gone and he collapsed, exhaustion claming his mind, and inducing a dreamless sleep.

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Carson had contemplated not telling Her what had happened, he knew She only tolerated him because he was a doctor, She would never like him, because he was military. It wasn't however worth the aggravation of not saying, She needed to be told.

So here he was, waiting in Meyer's office, waiting for her to deign to see him. And he was getting bored, he'd been waiting for half an hour, and he had patients to tend to. "Five minutes," he muttered, "five minutes and then I'm gone."

Four minutes later, Dr. Meyer wandered in, not bothering to apologise for her delay, sipping coffee, Beckettt barely contained his anger.

"You have something to tell me Dr. Beckett." Meyer stated, making it clear she was not asking a question, but making a demand,

"Aye, Colonel Sheppard came to see me earlier, he's not been sleeping for some time, I sedated him, so he could get some rest and he had some form of nightmare, he jumped out of bed and then collapsed."

"And you considered this of importance because?"

"Because he shouted Emily just before he woke up, considering he's not mentioned her by name in the last month I guessed there was some cause for concern. I believe he's punishing himself for her disappearance."

"And so he should," Meyer replied scathingly, "He _is_ the one who lost her. This is no concern of mine, except that she is found as soon as possible. Now I am very busy."

Beckett knew a dismissal when he heard one, so he got up and left, neglecting to acknowledge her.

"Bitch!" he fumed, as soon as he was out of earshot, and walked back to the infirmary to tend to his patients.

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	2. Chapter 2

Disclaimer: I don't own Atlantis, or anything related to it. I do however own the DVDs, about as close as I'll get.

A/N:Yes, I know this will make no sense, but please read and then understand. Also apologies, I was going through a phase of reading a lot of Elizabeth Chadwick books, hence the 12th Century England and France style.

Chapter 2

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Men barked orders at her in a language she didn't understand, she was grabbed roughly by the arm and hauled to her feet, disgust was evident on their faces as they noticed the blood matted in her short hair, the smell of human waste pervading their nostrils. Pushing her into a clean room, they left her with a tub of tepid water, and a rough cloth. Time, it seemed, to bathe.

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Guiding the horse round with his knees, shield on one arm, lance in the other, the Boy urged the horse into a gallop. He could feel the horse's muscles bunch under him as the roan gelding flew across the field. Moments before reaching his target, he rose up in the saddle, bracing his lance against his hip he struck the brightly coloured shield taunting him, the blow glanced off, it didn't hit the right spot, and he knew he was doomed, he tried to turn the horse away before the impact, but failed and was smacked on the back, and tossed from the saddle to the soft, muddy ground beneath.

Groaning he rolled to his feet and dusted himself off, his lord, Simon de Lenate, threw him a wineskin and went to reset the quintain.

"Don't worry lad, at least you can make it move now," He laughed, watching the boy go scarlet, "besides, you've been with me a senight, and came to me less than a boy, you'll do for now."

"Thank you my Lord," the Boy said, bowing.

"Come lad, the night is coming faster than we can move, time to eat."

Bowing again, the Boy took the reins of his horse, and led it back to the stable. Leaving him in the care of a groom, the Boy made his way across to the keep.

Lord Simon was a hearth knight, he had pledged fealty to a man by the name of Earl Thomas of Aberwyn, third cousin of King Richard. As a hearth knight, he had no fixed dwelling, he stayed wherever his lord did, and slept, as the title suggested, in the great hall by the fire with all the other knights in Earl Thomas' employ. As his Squire, the boy was of less importance and could sleep where he liked.

Crossing the courtyard between the stables and the hall, the Boy was aware of many eyes watching his progress. To his left he saw two of the kitchen maids nudge each other and giggle, a total lack of propriety being shown as they vied for his attention. To his right he saw a group of Earl Thomas' Squires, who eyed him with a mixture of anger and mistrust. Ducking his head, the boy near ran into the hall, desperate to be away from prying eyes.

He couldn't help attracting attention, his dark wavy hair reached just below his jaw, often falling over his face and concealing ice blue eyes. His colouring was rare, his skin was pale, his bone structure small, and wiry muscles were concealed easily under tunic and braies. It made him both interesting and attractive to women, and if truth be told, to men of a certain persuasion.

He climbed the steps into the hall, and seated himself at one of the lower trestles. Glancing at the dais he noticed the Earl was in residence, awaiting the birth of his latest bastard offspring no doubt. The Boy had only been with Lord Simon for a week, and in the area only a senight longer, yet three children had been born of the Earl's loins in that short space, it was rumoured his youngest mistress, of only fifteen, was in travail at this moment.

During his musings a bowl of pottage and day old bread had been placed in front of him, it was consumed as quickly as he could manage. Conversation went on around him but he didn't join in, his grasp of the language wasn't good enough yet, so he listened and picked up what he could in the hope of improving swiftly.

"Boy! Come to my table!" Lord Simon bellowed from across the room, "My squire does not sit by the door!"

He flushed scarlet, and left his table, hastening to the other side, hoping to be ignored. Sitting by his Lord, he was presented with more food, only this time he noticed his server. "Thank you," he said, quietly, and was rewarded with a small smile from the serving woman.

"So. Simon, who's the lad?" asked a stout, middle-aged man across the trestle.

"My new squire, Lord James, I believe him to be around fourteen years. Is he not a promising looking young man?"

"He is, he is." He turned to address the boy, "do you not have a tongue in your head lad?"

"He speaks but a small amount James, but I believe he understands more."

"I spoke to the Boy Simon, not you. What's your name lad? Come, speak!"

"Em…Liam my Lord, Liam el Trouney." It was the first name that had come into his head when Simon took him for a squire, it was similar enough.

More conversation followed, before Simon decided that it was late, "Go to bed boy, the stables should suit you." He was used to Liam's odd ways and penchant for sleeping alone, he thought it odd for a boy who had so much female attention, but he thought little of it.

Settling down in the stable by the gelding, Liam sighed, this was going to get very difficult, when asked for a name, the wrong one had very nearly came out, what would have happened? If the response had been "Emily my Lord, Emily Turner."

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Sparring, it took his mind off things, lashing out at Ronan he tried to beat the larger man. He feinted left, but struck right, landing a lucky blow to the lower stomach. Ronan grunted and swung back, catching John on the chin and making his head swim, a flick of his foot brought Sheppard down hard.

"You are not up to this, you still need rest." He said whilst extending his arm to pull John up.

"Yeah? Well I need to keep busy, stops me thinking."

"Some might say it doesn't take much." Ronan responded with a grin, "But I don't mind beating you up again if it makes you feel better."

"Great, I'm glad we understand each other."

The sparring match began again.

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This was definitely an improvement, clean clothes and fresh air; they went a long way to making her feel better. As she curled up to sleep in the hay, she thought, 'maybe tomorrow, the sun will rise again.'

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	3. Chapter 3

Disclaimer: I don't own Atlantis. 'Nuff said.

Chapter 3

John sat on his bed contemplating sleep, it hadn't been coming easily of late, and the nightmares had changed from visions of Elizabeth to images of Emily. After what happened in the infirmary a week ago, he just couldn't risk asking Carson for more sedatives, not that drugs were his first choice. He'd tried everything, running, working late, early mornings, he even considered jumping off the north pier for a quick swim, until Rodney pointed out that the water was so cold he'd die of shock before he managed to swim anywhere.

"Rodney!" John sprang to his feet, the scientist was never asleep, and since he'd been demoted he was always happy for company.

Wandering out of his quarters, he found the nearest set of stairs and set off for the research lab at the bottom of the main tower, walking killed time, and time was something he had a lot of at the moment.

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Laura Meyer was in her office going over the report of Emily's disappearance; she couldn't believe the incompetence of the military. Colonel Sheppard was one of her pet hates, his whole attitude irritated her, and he made it painfully obvious he would never accept her the way he had the wonderful Dr. Elizabeth Weir.

Her musings were cut short by an incoming transmission, glancing at the screen she noticed it was a secure channel requiring an authorisation code. Frowning she locked her door and entered the obligatory sixteen digit code.

"Confirm identity!" The expressionless voice demanded when the channel connected.

"Laura Meyer, fifteen seventy-three, alpha, four, one, six." She responded, keeping her voice neutral, any change of pitch would mean she was not alone, and the connection would not be made.

"Identity. Confirmed. Connecting."

"Meyer, good evening." A thin, blonde haired man appeared on her screen, "Time for your weekly report I think."

"Good evening, a very little to report I am afraid sir," Meyer replied, a edge of disgust in her speech, "Turner is still missing, the military are incompetent and that Sheppard man needs to be sacked!"

"We cannot move him Laura, you know that. He was placed by the military not by us, besides he as the ancient gene, he could yet be useful."

"All our people have had the ATA gene therapy sir, they.."

The blond man cut her off, "He's got the original gene, he's the only one that has successfully managed to operate the control chair, and other systems in the city work for him that don't work for anyone else! More to the point _WE _cannot dispose of him without attracting attention. Give it time, is he still unstable?"

"Yes, for the moment, but he appears to be improving, so I can't put him down as being unfit for duty."

"Ignore him then, we have more pressing matters to attend to. We're increasing speed, time for the next phase."

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To get to Rodney's new lab, Sheppard had to cross the control room, which at this time of night was practically empty, only the ghost watch was there, guarding over the city whilst it slept.

Out of habit he glanced up at Elizabeth's office, half expecting to see her busy at work or standing on the balcony, cup of coffee in hand. She wasn't there of course, but a light was on. Straining his eyes he could see Meyer sitting in front of her computer, seemingly talking to it, which was a crazy thought for sure, as the wormhole wasn't open, meaning no messages could be sent or received. 'She's going crazy' he thought, but stored the information away, determined to ask McKay about it when he saw him.

He turned away, preferring to keep moving than stay anywhere that was in her company. He mooched across the room, nodding to the team as he went, ignoring the curious looks at his odd behaviour. Pausing before the door he turned, a strange feeling raising the hair on the back of his neck, "Elizabeth?" he whispered as he looked at the gate, then an expression of immense sadness clouded his face, he sighed and shook his head before passing through the sliding door, and on down to Rodney's lab.

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Rodney McKay was analysing some results when there was a knock on the door and Colonel Sheppard walked in.

"Hey Rodney, what ya doin?"

"I'm analysing results, what does it look like I'm doing? Practising my tap dancing skills?" He snapped, irritated at having to do such a boring job, "More to the point, what are you doing, shouldn't you be in bed or something?"

"Yeah I guess so, but I was bored and couldn't sleep so I thought I'd come and annoy you." John responded with a trace of a grin. He enjoyed spending time with Rodney, he didn't have to worry about what he said, after all McKay hated Meyer as much as he himself did.

"You've been having problems sleeping for longer than this Emily thing haven't you? Since Elizabeth if I'm not mistaken." The air of nonchalance with which McKay said this would have made Sheppard hit any other man, but he knew it was said to disguise Rodney's own painful feelings.

"Yeah, but it's worse in a way now, I used to see her you know, but now it's Em, I guess you heard about the infirmary incident?"

"_Everyone_ heard about the infirmary incident," McKay answered, "I miss Em too you know, it's odd, with her it's kind of worse, she's still alive somewhere. I take it there's no news?" He asked hopefully.

"Nothing, it's been six weeks, and that whole planet has been scanned, Jumpers have covered every continent, the only living things there are of the plant variety." John responded dejectedly. "She isn't there."

"It wasn't your fault you know, if anything it was mine."

"Ok, I know you have a big ego Rodney, but how do take the blame for this one? You weren't even on the team!"

"Exactly. If I had been then she wouldn't have been there, thus she couldn't have been taken."

"But if Meyer hadn't reassigned you, you would have been there, so technically it's her fault." John countered, "Anyway, as a matter of interest, is it possible to receive transmissions when the gate is shut down?"

"Theoretically yes, but it would have to be bounced off several satellites, spaced equally between…" McKay began before he stopped and started to randomly type into his computer.

"Er, Rodney?"

"Shhhh! Concentrating!" After typing for several minutes he sat back with a grin on his face. "You weren't talking about the she-demon upstairs by any chance?"

"Well yeah but..."

"Well she's been receiving a lot of traffic about this time every week since she started, it's a secure channel that I don't recognise, and it's definitely not the SGC she's talking to, there's always an open wormhole for that. No this is coming from somewhere else." He began typing again, and John knowing better this time kept his mouth shut.

McKay started muttering under his breath, "Stupid, slow computers" seemed to be the main gist. Pushing off from his desk he grabbed cable and another laptop, deftly linking them together he started to type swiftly into one whilst waiting for a programme to load on another. After several minutes both computers were displaying a confusing amount of information. "What are you up to?" He muttered.

"What? Nothing!" Replied John dropping the stone he was playing with back onto the desk.

"Not you. But don't touch anything. No her, look." He turned the computers so that Sheppard could see the screens. The left screen showed a list of what appeared to be coordinates, most in black, but several in red, the right hand screen showed a complicated network of dots and lines stretched over what appeared to be a star map.

"So er, what am I looking at?"

"This here, is Earth," Rodney began, pointing at a dot in the bottom right corner of the map screen, "And this, is us." He pointed to the corner diagonally across from Earth. "These lines show the signal, the white lines, ignore them, they don't go anywhere, but the red lines, that's the path of the signal, and they correspond with the red coordinates here, these are points where the signal is boosted, so they must be ships or beacons of some sort, now if I'm right someone's gone to a lot of trouble to hide this signal, you see how they criss-cross? And bounce back to previous points? It's all done to try and confuse the computers, it's a good job I'm not a computer." He sat looking smug for a second before a strange look came across his face.

"Rodney? What's wrong?"

"The signal, it originates form Earth right? But it's not the SGC and the IOA don't have the technology to do this, nor do they have a reason."

"_AND?_" John prompted, knowing there was more to come from the man

"And, there aren't that many other people with access to this type of stuff, and even less can have ships and outposts stretched other such a large area. I think we need to consider that our 'leader' may be working for someone else."

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	4. Chapter 4

Disclaimer: As always, Atlantis is not mine.

Authors Note: More medieval-ness, if you don't like it, this story is probably not for you.

Chapter 4

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Awakening before the birds began to sing; Emily rubbed the sleep from her eyes and grabbed her rough cloth towel. Just because she slept with the horses did not mean she intended to smell like one. Wandering down to the river she stripped and waded into the water. It had been a month or more since she became Liam el Trouney, and she was fitting into the life of a squire well. But moments like these were dangerous, to be female was difficult, the life was to be a servant or a whore, unless you were of noble birth. She washed and dried as quickly as possible and returned to the camp.

They'd moved from Earl Thomas' within the last week, and were on their way to lay siege to a castle in the North. Rebellion was stirring, and several factions had bonded together in mutual hatred of King Richard. Richards own brother, Henry, had sided with the rebels, making childless Richard reconsider his heir. Thomas, as Richard's oldest and closest male relative, was the obvious choice.

The fortnight spent at Thomas' keep however would not prepare Emily for the forthcoming battle, whilst Lord Simon promised to keep his lad safe, there were no guarantees. 'A baptism by fire' Emily mused, 'or by blood.'

Whistling, she entered the camp and began kicking her companions awake. They had happened upon a village where the local ale-wife had just finished a fresh brew, the men, using the excuse that it would sour in the heat, had drunk the house dry and were now suffering the effects. Many a thick head would be experienced this morning. Smiling to herself she whistled louder, eventually having to stop as she couldn't continue for laughing, groans and complaints washed over her as she wandered over to the food tent to break her fast.

"Fair morning young one," smiled the cook, displaying his remaining teeth. "I have a fresh batch of cinnamon bread with your name on it if you're interested?"

"Fair morning Damon, and I am very interested, thank you." She reached for the bread the old man was handing out. "Damon," she enquired, "how old are you?"

"Forthright young man aren't you?" he laughed, "but you're free enough to ask, I've more years than three score, but less than Emmeline." Emmeline was the camp midwife, and in high demand. Much of the camp followers were made up of wives and whores, both groups in constant need of a midwife, especially in a camp this large. The old woman was very knowledgeable, but also very old, and the odds of her living much beyond her current age were slim indeed.

Conversation moved onto the upcoming battle, rumour had it that the King's brother Henry was actually _in_ the castle they were to lay siege to. If he was killed in the fight, Thomas' place as the future king was practically guaranteed.

By the time she had washed her cinnamon bread down with watered wine the camp was moving, albeit somewhat unsteadily.

"Boy!" Lord Simon bellowed from the tent flap, making several men wince, "thick-headed this morning are we?" he ignored the other men, addressing only Emily.

"No my Lord, I was from my bed afore the sun, I have washed and broken my fast, and I go to tend my horse sir." Bowing, she left the tent.

"The boy needs to bed something if you ask me," said one of the men, Evan el Sellit, "there are plenty on women, why does he not take one?"

"Hold your tongue, el Sellit," Simon spat, "he's fine as he is."

"Yes," replied Sellit, "very fine, maybe he prefers to be a _fine_ lad to the older men, rather than a strong man to the women." Loud guffaws greeted his comment, and Simon stormed out of the tent.

His search for the boy was cut short as it was announced that they must break camp immediately, word had been sent that Prince Henry intended to hire more men to defend the keep, if they intended to lay siege, they must reach it within the week.

Simon swore and ran to the stable, only to find his horse fully clad in saddle and rein, Emily's gelding the same. The packhorses were nowhere to be seen, hurrying over to where his tent was pitched, Simon saw Emily demolishing it with much haste.

"Liam, I take it you've heard?"

"Yes my Lord, messenger was talking to the Earl as I walked by, I took the liberty of pre-empting your actions, I hope that is acceptable." Emily continued to work as she talked, her liege lord haphazardly gathered blankets and pots. Emily grimaced; he was making more work for her doing it like that, "My lord, would you not be better talking to the Earl? I believe he intends to send for all his knights."

"Of course boy, of course, you will be alright here?" Simon replied, hurrying off to see the Earl before Emily even had time to answer. Smiling to herself, she continued to pack, grateful to no longer be hindered.

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In the Jumper bay, Ronan was grumbling. John didn't think he'd ever known him to grumble before, brood yes, but never grumble. He wanted to go to the mainland, it had been weeks since he'd seen Teyla and he was getting tetchy. To be honest John was looking forward to the trip too, it would be nice to see her again.

"You ready?"

"Yes John, I've been ready for an hour."

"Ok then."

Sitting down at the controls John let his mind wander, last time he'd been over to the mainland Emily had been with him. He pushed the thought away, it was too painful, and besides, he'd never drive the Jumper in a straight line if he didn't concentrate. Guiding it smoothly out of the hanger, he glanced over at Ronan, "This is nice, just like old times," he said.

"If it were old times Sheppard, Teyla and Dr McKay would be with us, and Dr Weir would be waiting for our return."

"Yeah. I guess you're right."

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	5. Chapter 5

Disclaimer: Atlantis is not mine. I'd love to have a jumper though….

Chapter 5

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Lieutenant Colonel John Sheppard, military commander of Atlantis, had a desk. He had become a paper pusher, what an embarrassment. Elizabeth would have loved to see this. The sad thing was, he hadn't even seen it coming, I mean sure he'd not been on any missions since Emily disappeared, but he just figured that Beckett had signed him off. No such luck, somehow word must have filtered back to his superiors about his apparent inability to file paperwork correctly, it was the only explanation. Either that or they just wanted to torture him. Which was also a theory worth considering; he was renowned for not obeying orders after all.

He considered the pile of mission reports on the desk, it never seemed to get any smaller, "No wonder Elizabeth never got any time off." He said to himself, reaching for the next in the stack, it was going to be a long day.

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Teyla stretched out her unused muscles, being on the mainland had its disadvantages, not being able to train was one of them. Ronan's decision to stay on the mainland for a short time changed that situation rather. Colonel Sheppard had described him as having 'itchy feet' neither Teyla nor Ronan could quite understand the reasoning behind the statement.

"Ready?" Ronan questioned, as he shook out his own limbs.

"I am ready. Are you?"

He grinned his response and crouched into a fighting stance. Not long into the fight Teyla realised how rusty she had become, and how Ronan was compensating for it. "Do not hold back, or I shall never improve." She panted, ducking under his arm.

"Possibly, but if I don't you'll end up on the floor."

"Oh I count on it." She responded mischievously, "How else will I ever learn?"

Laughing Ronan caught her by the arms and swept her feet from under her, landing her on the ground with a bump. Releasing her arms he let her regain her feet. "Better?" he asked.

"Much, thank you. Again?"

"With pleasure."

Four bouts later and Teyla was exhausted. It was rare that she could beat him at peak fitness, there was no hope at the moment. "I am exhausted, I must quit now."

"Ok. Is there food? I'm hungry."

"Yes Ronan," Teyla said laughing, "There's food."

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Rodney checked his computer logs, he'd been running the tracer programme in the background ever since he'd first found the signal, he was trying to pinpoint the exact location of the origin, but so far he'd only managed to pinpoint Earth, which wasn't much of an achievement. According to his readings, there had been several of these incoming messages within the last fortnight, which was bizarre. Previously there had been only one occurrence per week of the peculiar signal, this increase could be signalling something else, something bad.

Suddenly the signal became active, picking up the trace, McKay grinned to himself. Live transmissions were easier to track, and they could be recorded. Seconds ticked by, and then he had it. The origin. He picked up the headphones and listened to some of the conversation.

"Oh crap." He said as he realised what it meant.

"I have to tell Sheppard." Grabbing the recording from his computer he ran from the room.

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Smiling to herself, Dr Meyer shut off her computer ran through her mental "to do" list. The plan had been stepped up, and the time was nearly here to complete it. Her superiors wanted Atlantis, and the city would be theirs.

The removal of key members of the Atlantis staff had been tricky to arrange, but achievable. A few well phrased conversations, 'accidentally' miss-sent disciplinaries and one or two direct re-assignments meant that the flagship team, and those most loyal to Earth, were all set to be sent away from Atlantis permanently.

It was time for the final stage.

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Rodney hurtled down the hallway in a distinctly ungainly manner; not being the most coordinated member of Atlantis had its drawbacks, for example the fact that he nearly trampled Lieutenant Cadman. Adamant to know why he'd nearly flattened her, she demanded he explain what his rush was. McKay refused to stop, but yelled for her to follow him if she really wanted to know. Cadman followed, shaking her head.

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"One more to go." John said to himself as he reached for the last report on the pile, it had taken him all day to get through the reports and he was seriously considering handing in his resignation after this. "So, MX12-743, what do you have for me today?" He mumbled, opening the file.

He barely reached the second sentence of the report when a very sweaty and out of breath Rodney McKay crashed through the door, closely followed by a grumpy looking Laura Cadman.

"Er hi guys!" John said with a mixture of amusement and confusion, "what's up?"

"I……..saw" Rodney panted, "I………saw."

"Saw what McKay?"

"Not me obviously," Cadman grumbled, "he practically trampled me to death in the corridor just now."

"Can she be here? " John asked, gesturing at Cadman, "I mean, is it important."

Rodney gulped air for several seconds before answering, "She's fine, we're gonna need all the people we can get on our side when this gets out."

"When what gets out?" Cadman asked looking confused, "what's this about?"

Rodney ignored her and plugged the disk into John's computer. "Shut the door, and lock it please." He told John. Glancing across to check it had been done, McKay started the recording he'd taken from Meyer's conversation.

"………_It's well under way now sir." _

"_Good to hear. Have you arranged everyone's removal?"_

"_Yes Sir. That McKay man is to be re-assigned to Earth in a few days, and I think he'll jump at the chance after being cooped up in the bowels of the city for so long. Sheppard and Beckett are to be sent to another base in Afghanistan. The Athosian woman and that other one appear to have left us of their own volition."_

"_Excellent work, and the others?"_

"_They're working well, the city is nearly ours sir."_

"_Good to hear. I'll check in with you again in eight hours."_

Sheppard and Cadman listened to the recording with somewhat glazed expressions. John spoke first.

"What was that?" he asked incredulously.

"The question is less what than who, the man whose voice you heard? That's Erik Van Leigh." Rodney countered.

"Er. Who?" John asked, feeling foolish and irritated all at once.

"Erik Van Leigh." Cadman responded before Rodney got the chance, "He's the CEO of the Van Leigh Software House, they create very sophisticated computer graphics systems, as well as some kick ass games, you must have played…….."

"Yes, yes, yes." Rodney interjected, "But their 'kick ass games' aren't what we should be bothered about." He accessed the military database and pulled up a few more documents on the screen. "I recognised his voice because I had a friend that worked at his company, I say worked because the company had a huge overhaul of all it's high ranking employees about a year ago, Van Leigh had a press conference saying there had been a security leak and that certain key members of personnel were no longer trustworthy, he ruined a lot of lives. Anyway my point, Van Leigh made this decision after being away on vacation for six months, he went from being a remarkable leader who was concerned about the welfare of every person on his staff, to the demon headmaster! All the most trusted people were fired."

"_AND?_"

"Demon headmaster?" Cadman queried.

"Kids book in the nineties about this guy who hypnotised children and wanted to take over the world." John responded before prompting Rodney again.

"AND, he's been linked, very recently I might add, with Farrow-Marshall Aeronautics."

He looked at the blank expressions of the two officers and sighed.

"Farrow-Marshall aeronautics was implicated by SG1 as being linked to the Trust, their new leader was Baal."

"So this means what exactly?" Cadman asked; her expression troubled.

"It means, there is a very strong possibility that our own 'good doctor' is working for the Trust."


	6. Chapter 6

Disclaimer: Atlantis, not mine, if it was I'd be much happier

A/N This chapter takes a lot of liberties with believability (Emily's plan), but then it is fiction.

Chapter 6

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Emily was checking her weapons, making sure they were clean and well oiled. There was a battle on the horizon and fear sat heavy in her stomach. The siege had been going well for over a month, but under the cover of night reinforcements had slipped around King Richard's men, and Henry's keep was bristling with over two thousand soldiers. Supplies were low outside the walls and Henry could probably taste victory in his fine wines.

But Emily was not stationed outside the walls; she was in the woods with the majority of the infantry and cavalry. The King had deemed her ideas on drawing Henry out onto the battlefield, the more sensible option. Six months of war strategy games with Sheppard had its practical uses after all. She had approached her Lord the night before they reached Avery castle; after having being part of the troupe sent to scout the route ahead she'd seen the castle for herself; and suggested they send only the least able fighting men. She smiled as she remembered the conversation.

"_The least able you say?" Lord Simon enquired, "for what purpose?"_

"_To draw them out my Lord, the keep is well fortified, with a good supply route over the river, here." She drew a rough map in the dust at their feet, "They will wear us down to our last supplies before we manage to even dent their armour."_

"_The boy knows nothing." Sneered El Sellit, "He's still green and has never seen fighting, he's afraid."_

"_Bite your tongue boy!" Lord Simon snarled, "or do you forget you are also an El, making you a squire too, you are not a knight yet boy, for all your Father's 'encouragement'." Turning back to Emily, he gestured for her to continue._

_Emily continued her map for a few moments, adding woodland and roads. "we approach along here," she said motioning to one of the roads she had drawn, "they will see us before we come round the corner, assess our number and decide how long our supplies can last. Any chatelaine worth her salt will know how much food to order to keep the army fed until ours are weak and exhausted. They will see us tomorrow at midmorning, we will not reach them until the following dawn, to seal off the supply route to the river will take a lot of time and man power and we will still not catch them before their supplies come through, we will be lost Sir."_

_A small crowd had gathered whilst she had been speaking, her clear, high voice carrying over the gruff sounds of the men._

"_So what do you propose?" a deep voice enquired, causing Emily to look up from her map in surprise. _

"_Sire, forgive me I did not see you." She stammered, recognising Richard._

_The young King smiled and pushed his hand through his shoulder length red hair, "Would you have not voiced your concerns had you known I was present?" _

"_On the contrary Sire, I would have taken my concerns to you first." She smiled back._

"_Good to hear, anyway, your propositions?"_

"_Yes Sire." She began again, "As they will see us so soon, and we shall be so powerless to stop their supplies, I believe, if what I have heard about Lord Henry is true," She paused and looked at the King, who inclined his head a fraction to agree with her, "Then he will desire to finish us, he will wait it out then charge full force when he believes us too weak to make much of a resistance. He will take the cowards path and slaughter exhausted men." She stopped when she heard a low growl from deep within Richard's throat and a collective intake of breath, believing she had perhaps indeed over-stepped the boundary concerning the King's brother she hung her head._

"_Continue boy," Richard urged, "However I believe I know your destination, I can scarce believe I did not realise my Brother's shortcomings myself, I am not angry with you."_

_Sighing with relief Emily resumed speaking, "My suggestion Sire is that we send men not suited to the battle field, those who can operate siege machinery but are not good in close combat. If we send them with few pack-horses but full armour and weaponry, your Brother may yet believe you are the coward, who sends ill equipped men into battle with no hope of survival." She did not pause this time as the men around her cringed at her words concerning the King's honour, "The elite, infantry and cavalry we leave here," She pointed at a densely wooded area out of the vision of the keep, "with the remainder of the supplies we can have men strong and ready for Henry,"_

"_Who will ride out when the small contingent has weakened, determined to finish them," Richard continued as she paused to breathe, "they can retreat as the doors open, drawing Henry out further and we meet him here," He pointed to a large area of flat land between the castle and the woodland, "Henry is a bad leader, organising his troops on a battlefield will be a near impossible task for him. An all out battle, we will finish him."_

_The end of the King's speech was greeted with cheers and exclamations of "Remarkable plan Sire."_

_Emily smiled and discreetly slipped away._

That had been nearly a month ago and the plan was working perfectly. On the morrow they would charge onto a battlefield of their choosing, and hopefully defeat their enemy. Emily was not looking forward to having to kill, but it was a part of who she had become, and she would not shirk her duties. Placing her weapons on her pallet, she rose to tend to her horse.

As thanks the King had presented her with a new warhorse, he was a big animal at a little under eighteen hands, and his coat was so pale a grey that he looked almost silver, mane and tail were pure white, making the stallion worth a sum that exceeded what a hearth knight could earn in three years. "Don't you die on me tomorrow, do you understand?" she muttered to the horse, before burying her face in his long mane.

The morning of the battle was cold; it felt as though the flames of Hell itself had been extinguished. Emily cupped her hands around the mug of hot spiced cider and finished chewing the last of the warm cinnamon bread Damon had given her. The old man had left with the last of the baggage train only a half hour earlier, the safety of the women, children and elderly was secured, the were away from the battle and yet close enough still to tend to the wounded when the battle was through.

Draining the last of her drink, Emily stood and moved further into her tent. Dressed as she currently was she would last only seconds on the battlefield, a soft wool tunic would be cut through easily, allowing the enemy to carve meat from bone beneath. However being as she was only a squire, she was considered less valuable than the knights around her; protection consisted of merely a thickly padded gambeson and chausses.

"Liam, where are you boy?" Lord Simon called with a muffled shout, whilst struggling to heave his hauberk over his head. Emily hurried to his side and took the knee length mail shirt from his hands.

"My Lord, what are you doing?" she demanded with barely concealed amusement, "you'll do yourself a mischief trying to put this on on your own." She pulled a stool forward and ordered Simon to sit whilst she hefted the shirt over his head. Simon bristled and groused about disrespect as he stood and jigged the hauberk into place. Emily's deft hands made short work of buckling his chausses and sword belt into place, she was about to fling his surcoat over his mail when Simon stopped her and took it himself.

"This part I can do myself." He said as he pulled the silk tunic over his head. Emily watched the red and grey silk shift and settle, marvelling at the beauty of the essential item. When she first saw the surcoat, she had assumed it was Simon's dress robe, but when he explained to her it was for use in battle she didn't understand. He told her it had three main uses, the first to identify which side you were on, in battle the lines become blurred and it easy to lose sight of who is the enemy. The second use, he told her, is to identify your body should you lose your head, he explained that each coat was different, all carried your liege lord's crest and an identifying mark, Simon's was a black arrow on the left shoulder. The final use though, he said, was the most important. The silk covered the mail and stopped it heating up too much in the sun, too much heat on the metal rings could cause them to heat so much they could not be touched, being unable to remove one's hauberk in the intense heat after battle, combined with the fact that the quilted gambeson has caused the knight to sweat, altogether it could result in the knight's death. And to boil to death in your own armour is not an honourable or pleasant way to die.

"Liam!" Simon shocked Emily back to reality, "are you listening to me boy?"

"Sorry my Lord, I was just…thinking."

Simon's expression softened and he grasped his squire's shoulder in an awkward gesture of comfort. "It will not be easy lad, I cannot lie to you. But I can promise you that I will do all I can to keep you safe."

Emily's response was cut short by the call to arms. Earlier fear and excitement had fought for control, but now they both lay heavy in her belly as she quickly collected her weaponry and gathered her horse's reins. Squaring her shoulders and swallowing hard she followed Simon to the battle line.

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"The Trust?!" Cadman exclaimed. "Why…What...I don't understand Rodney!"

"The Trust." Rodney stated, slowing down his speech as though speaking to a child, "Nasty, horrible people, who want Atlantis for themselves. They put a Goa'uld in Colonel Caldwell….Remember?"

"I know who they are Rodney," Cadman replied scathingly, "And I'm not a child. I just don't understand how they got here, or what they're doing, or what we're going to do about it!"

"I'll tell you what we're going to do," John interjected before they started arguing, "We're not gonna let them have Atlantis. If Elizabeth were here, she would've fought, and when she couldn't fight anymore she'd have blown the city to pieces rather than let them have it. We fight and for that we need Teyla and Ronan."

"And Carson." Rodney added.

"Why?"

"Babies…mainland…excuses…oh whatever let's go!"

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